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Protein Structure

Proteins are full of repeats

Protein structure is made of repeated elements like helices, and strands. Comparing protein structures is the way scientists learned the elements of protein structure.

This 45-minute activity asks students to compare three protein models and three water models. 

The activity teaches:

  • Secondary structure: helices, sheets, and turns

  • 4 common representations of protein structure

  • Protein "space" size relative to water size

  • How tertiary structure is stabilized

  • How proteins interact with their environment

Where's the data?

Want to know if the activity is effective? We did too. Check out our peer-reviewed publication here.

The Models

4 individual models

  • Crambin, a seed storage protein

  • Cytochrome C, with heme

  • Lipoprotein Signal Peptidase II, with 4 helix representations 

  • 3 water molecules

All model files provided are to scale. Use caution when printing from .stl files, which are dimensionless. Water molecules are connected, after printing, cut the wire connecting each water.

 

Model design: Michelle Howell

Cytochrome C

Printable File Downloads 

Opens a UNL Digital Commons page with download files at the bottom. Two versions available: .blend and .stl

Note that your printer needs to be able to print support material.

Print Cytochrome C at Shapeways

No 3D printer? Print models with a professional service, they ship to your door.

 

Model design: Michelle Howell

Crambin

Printable File Downloads 

Opens a UNL Digital Commons page with download files at the bottom. Two versions available: .blend and .stl

Note that your printer needs to be able to print support material.

Print Crambin at Shapeways

No 3D printer? Print models with a professional service, they ship to your door.

Model design: Michelle Howell

Lipoprotein Signal Peptidase II

Printable File Downloads 

Opens a UNL Digital Commons page with download files at the bottom. Two versions available: .blend and .stl

Note that your printer needs to be able to print support material.

Print Lipoprotein at Shapeways

No 3D printer? Print models with a professional service, they ship to your door.

Model design: Michelle Howell

Water at Scale

Printable File Downloads

Opens a UNL Digital Commons page with download files at the bottom. Two versions available: .blend and .stl

Note that your printer needs to be able to print support material.

Print Lipoprotein at Shapeways

No 3D printer? Print models with a professional service, they ship to your door.

Model design: Michelle Howell

 
The Activity

We recommend a printed version only for small classes and a combination of printed and interactive online activity for large classes. 

This 45-minute activity is designed to replace a lecture-style class on protein structure. In our class of >110 students, it was completed in groups of three. 

Activity learning goals:

  1. Different ways to represent protein structure

  2. How amino acids of a protein interact to make “secondary structures”

  3. How amino acids of a protein interact to make “tertiary structures”

  4. How proteins interact with solvent

  5. Why protein flexibility is important

  6. How protein regions can be made more stable or more flexible

Protein activity2.PNG
 
The Slides

These slides describe:

  1. Prerequisite class knowledge

  2. An introduction to why protein structure is important

  3. Model description

  4. Clicker question

  5. Protein methods image

  6. A summary of what our classes should know about amino acids

 
Looking for Assessment Questions?

Or activity answer keys? Our data suggests that students will perform better on typical biochemistry test questions regarding protein structure after doing this activity. However, Dr. Roston is happy to provide assessment questions and answer keys.

Contact Dr. Roston

Questions? Comments! Talk to us